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(-) Description

Title :  SOLUTION STRUCTURE OF THE PH DOMAIN OF PROTEIN KINASE C, NU TYPE FROM HUMAN
 
Authors :  H. Li, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  13 Dec 05  (Deposition) - 02 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ph Domain, Protein Kinase C Nu Type, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Li, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Ph Domain Of Protein Kinase C, Nu Type From Human
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN KINASE C, NU TYPE
    ChainsA
    EC Number2.7.1.-
    EngineeredYES
    Expression System PlasmidP050711-24
    Expression System Vector TypePLASMID
    FragmentPH DOMAIN
    GenePRKCN, EPK2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymNPKC-NU, PROTEIN KINASE EPK2

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2D9Z)

(-) Sites  (0, 0)

(no "Site" information available for 2D9Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D9Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D9Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061532L445IKPCD3_HUMANPolymorphism55912911AL36I
2UniProtVAR_037149Q546RKPCD3_HUMANPolymorphism17856887AS128R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.KPCD3_HUMAN416-532  1A:8-123

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003790663ENSE00001479696chr2:37545037-37544930108KPCD3_HUMAN-00--
1.4bENST000003790664bENSE00001479694chr2:37544322-37543380943KPCD3_HUMAN1-96960--
1.5aENST000003790665aENSE00001706811chr2:37520414-37520276139KPCD3_HUMAN97-143470--
1.6aENST000003790666aENSE00001758269chr2:37518142-37518011132KPCD3_HUMAN143-187450--
1.7ENST000003790667ENSE00000747393chr2:37516656-37516499158KPCD3_HUMAN187-239530--
1.8bENST000003790668bENSE00000747391chr2:37513512-37513320193KPCD3_HUMAN240-304650--
1.9aENST000003790669aENSE00000747390chr2:37509762-3750968578KPCD3_HUMAN304-330270--
1.10ENST0000037906610ENSE00000747389chr2:37507072-37506889184KPCD3_HUMAN330-391620--
1.11bENST0000037906611bENSE00001802809chr2:37505132-37505009124KPCD3_HUMAN391-432421A:1-23 (gaps)40
1.12ENST0000037906612ENSE00000747387chr2:37502987-3750291078KPCD3_HUMAN433-458261A:24-4926
1.13aENST0000037906613aENSE00000747386chr2:37501840-37501564277KPCD3_HUMAN459-551931A:50-129 (gaps)89
1.14aENST0000037906614aENSE00000747385chr2:37499575-3749952353KPCD3_HUMAN551-568180--
1.15aENST0000037906615aENSE00000747383chr2:37496830-3749675873KPCD3_HUMAN569-593250--
1.16ENST0000037906616ENSE00000747381chr2:37494679-37494573107KPCD3_HUMAN593-628360--
1.17bENST0000037906617bENSE00000747379chr2:37487527-37487366162KPCD3_HUMAN629-682540--
1.18ENST0000037906618ENSE00001604113chr2:37486824-3748672699KPCD3_HUMAN683-715330--
1.19bENST0000037906619bENSE00000747375chr2:37484072-37483805268KPCD3_HUMAN716-805900--
1.20ENST0000037906620ENSE00000747374chr2:37481432-3748134786KPCD3_HUMAN805-833290--
1.21bENST0000037906621bENSE00001479657chr2:37480493-374776452849KPCD3_HUMAN834-890570--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:129
 aligned with KPCD3_HUMAN | O94806 from UniProtKB/Swiss-Prot  Length:890

    Alignment length:155
                                   402       412       422       432       442       452       462       472       482       492       502       512       522       532       542     
          KPCD3_HUMAN   393 STSNNIPLMRVVQSIKHTKRKSSTMVKEGWMVHYTSRDNLRKRHYWRLDSKCLTLFQNESGSKYYKEIPLSEILRISSPRDFTNISQGSNPHCFEIITDTMVYFVGENNGDSSHNPVLAATGVGLDVAQSWEKAIRQALMPVTPQASVCTSPGQG 547
               SCOP domains d2d9                 za_ A: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------2d9zA01 A:8-129 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-----------------....eeeeeeeeee......eeeeeeee..eeeee.........eee.....eee.................eeeee...eeee...................hhhhhhhhhhhhhhhh---------...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------I----------------------------------------------------------------------------------------------------R- SAPs(SNPs)
                    PROSITE -----------------------PH_DOMAIN  PDB: A:8-123 UniProt: 416-532                                                                             --------------- PROSITE
               Transcript 1 Exon 1.11b  PDB: A:1-23 (gaps)          Exon 1.12  PDB: A:24-49   Exon 1.13a  PDB: A:50-129 (gaps) UniProt: 459-551 [INCOMPLETE]                            Transcript 1
                 2d9z A   1 GSSG-----------------SSGMVKEGWMVHYTSRDNLRKRHYWRLDSKCLTLFQNESGSKYYKEIPLSEILRISSPRDFTNISQGSNPHCFEIITDTMVYFVGENNGDSSHNPVLAATGVGLDVAQSWEKAIRQALM---------SGPSSG 129
                               |     -         - |      13        23        33        43        53        63        73        83        93       103       113       123       124     
                               4                 5                                                                                                                   123       124     

   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D9Z)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (KPCD3_HUMAN | O94806)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004697    protein kinase C activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires diacylglycerol.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0007205    protein kinase C-activating G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds with activation of protein kinase C (PKC). PKC is activated by second messengers including diacylglycerol (DAG).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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